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- PDB-6m4j: SspA in complex with cysteine -

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Basic information

Entry
Database: PDB / ID: 6m4j
TitleSspA in complex with cysteine
ComponentsSspA complex protein
KeywordsOXIDOREDUCTASE / cysteine desulfhydrase
Function / homologyAspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / 3-Layer(aba) Sandwich / Alpha Beta / CYSTEINE / PYRIDOXAL-5'-PHOSPHATE
Function and homology information
Biological speciesVibrio cyclitrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, L. / Gao, H.
CitationJournal: Mbio / Year: 2020
Title: Structural Analysis of an l-Cysteine Desulfurase from an Ssp DNA Phosphorothioation System.
Authors: Liu, L. / Jiang, S. / Xing, M. / Chen, C. / Lai, C. / Li, N. / Liu, G. / Wu, D. / Gao, H. / Hong, L. / Tan, P. / Chen, S. / Deng, Z. / Wu, G. / Wang, L.
History
DepositionMar 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SspA complex protein
B: SspA complex protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5326
Polymers75,7952
Non-polymers7374
Water15,547863
1
A: SspA complex protein
hetero molecules

A: SspA complex protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5326
Polymers75,7952
Non-polymers7374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
2
B: SspA complex protein
hetero molecules

B: SspA complex protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5326
Polymers75,7952
Non-polymers7374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
Unit cell
Length a, b, c (Å)132.264, 132.264, 152.636
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-921-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.8708, 0.491563, 0.008509), (-0.491635, 0.870707, 0.012785), (-0.001124, -0.015316, 0.999882)-0.05609, -0.02877, -38.628262

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Components

#1: Protein SspA complex protein


Mass: 37897.465 Da / Num. of mol.: 2 / Mutation: C314S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cyclitrophicus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 863 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsThe sequence has been deposited to NCBI with accession code WP_016789103.1. And C314S mutation was introduced.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.8M ammonium citrate, pH 7.0 / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 1, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.8→115 Å / Num. obs: 72776 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.962 / Net I/σ(I): 5.3
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 11922 / CC1/2: 0.962

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VAX

3vax


Resolution: 1.8→114.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.106 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.106
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 3655 5 %RANDOM
Rwork0.1657 ---
obs0.167 68787 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 63.79 Å2 / Biso mean: 22.156 Å2 / Biso min: 12.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å2-0.71 Å20 Å2
2---1.42 Å20 Å2
3---2.13 Å2
Refinement stepCycle: final / Resolution: 1.8→114.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5297 0 44 863 6204
Biso mean--21.04 32.28 -
Num. residues----694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025556
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9627573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28224.918244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07615924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.61525
X-RAY DIFFRACTIONr_chiral_restr0.1440.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214239
X-RAY DIFFRACTIONr_rigid_bond_restr1.97335556
X-RAY DIFFRACTIONr_sphericity_free30.401557
X-RAY DIFFRACTIONr_sphericity_bonded16.97756236
Refine LS restraints NCSNumber: 537 / Type: TIGHT THERMAL / Rms dev position: 3.24 Å / Weight position: 0.5
LS refinement shellResolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 248 -
Rwork0.207 4640 -
all-4888 -
obs--99.09 %

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